Foragers show adaptive responses to changes within their environment, and such behavioural plasticity can be a significant driving force in speciation. We investigated how lactating Antarctic fur seals, Arctocephalus gazella, adapt their foraging within two contrasting ecosystems. Location and diving data were collected concurrently, between December 2003 and February 2004, from 43 seals at Bird Island, where krill, Euphausia superba, are the main prey, and 39 at Heard Island, where mostly fish are consumed. Seals at Heard Island were shorter and lighter than those at Bird Island and they spent longer at sea, dived more frequently and spent more time in the bottom phase of dives. Generalized additive mixed effects models showed that diving behaviours differed between the islands. Both populations exploited diel vertically migrating prey species but, on average, Heard Island seals dived deeper and exceeded their estimated aerobic dive limits. We propose that the recovery of the Heard Island population may be limited by the relative inaccessibility and scarcity of food, whereas at Bird Island, the presence of abundant krill resources helps sustain extremely high numbers of seals, even with increased intra- and inter-specific competition. Both populations of fur seals appear to be constrained by their physiological limits, in terms of their optimal diving behaviour. However, there does appear to be some flexibility in strategy at the level of trip with animals adjusting their time at sea and foraging effort, in order to maximize the rate of delivery of energy to their pups.